I'm going to try and address these point by point.
1. There are some books of the bible where the authors are clearly identified. There are others where the authors are speculated, but we don't really know for certain. It's possible (and I'm using possible in its REAL sense here--after all, anything is possible in a quantum universe)...it's possible that some of the books were written by women. Unlikely, but possible. It's also possible that women didn't do the writing, but highly influenced the writing of certain books. For example, it's very possible that Luke worked closely with Mary, the Mother of Jesus in the writing of his gospel. After all, it contains passages with very personal information about Mary becoming pregnant, about Joseph's response, etc.
So, the idea that God used primarily/entirely men to write the scriptures doesn't (to me) demean women in any particular way.
2. The counting of men and male children had to do with the cultural value placed on these children. It wasn't God-ordained. There are lots of cultures that place a higher value on boy children than girl children. The fact that the Hebrews engaged in this kind of system doesn't necessarily reflect the heart of God, IMO, but the will of humanity.
3. While the rape-law you specifically mentioned seems barbaric to our modern sensibilities, it was actually not at the time. While primitive and imperfect, it did provide a means of justice for the young woman. After being raped, it is unlikely that she would marry, so demanding that the rapist pay her brideprice would provide for her as an unmarried woman or that he marry her and provide for her did provide a level of justice. The message was "You MEN will be held responsible for this."
The issue with wifely adultery was obviously paternity. While all adultery was wrong (look at the Ten Commandments), a husband cheating on his wife doesn't bring the paternity of the children into question.
I believe God always valued women (even if men didn't). And he proved this when Jesus (God) walked on earth. He valued women in so many different ways...some that conflicted with the culture and the Pharisees (the woman caught in adultery, for example). Of course, I think the best example of God's view of women is that he chose a woman to birth our Savior. God could have manifested a Savior in any number of ways. However, he chose to have a very humble woman give birth to Jesus (and raise him, mind you). This alone elevates womanhood, in my view.
Of course, there is also the scripture mentioning "no male or female, no Jew or Greek..." God is no respecter of persons. He doesn't place a higher value on someone because they might be rich, or a certain ethnicity, OR a certain gender.
From a personal level, I know how gracious and kind God has been to me. While I have sometimes had conflict with some Christian men who insist this and that about women, I have always felt God's loving approach toward me and my feminine self.